Rishi De-Kayne

This framework could help us move from serendipitous discovery toward predictive identification of bio-utility across the tree of life. Read the full perspective for the details. [8/8]

Evolution tells us not just what's useful, but where to look next, highlighting lineages that might harbor untapped potential for biotechnology applications. [7/8]

But protein data alone isn't enough. Integrating evolutionary relationships between species with this protein information helps us understand where useful functions evolved, distinguish conservation from convergence, and spot breakthrough novelty in constrained protein families. [6/8]

The key? Identifying indicators of bio-utility from protein variation itself:
• Proteins with extreme properties (like extremophile polymerases)
• Proteins with discrete novel functions (like different proteases)
• Proteins showing conserved or convergent functions (like antifreeze proteins) [5/8]

Schematic of information that can be leveraged for finding and interpreting bio-utility, including a gene tree, the characteristics of proteins simplified into a 2D protein surface, and the evolutionary relationships between the species in which the same proteins evolved, highlighting the wealth of knowledge and broader perspective we gain about proteins when we include their evolutionary information.

We propose an evolution-integrated framework that combines the best of both worlds: expanding sampling breadth while more deeply interrogating existing data through an evolutionary lens. [4/8]

Biology needs to become prospective Since biological data are often non-independent, more data doesn't always mean more insight. We argue that a prospective approach is needed to uncover the deepest principles of life.

In silico bioprospecting tries to fix this by mining existing databases. But those databases are taxonomically biased (see another one of our pubs dropping today: thestacks.org/publications...), and the methods often require knowing what you're looking for upfront. [3/8]

Bioprospecting has given us incredible discoveries, from life-saving drugs to agricultural innovations. But traditional approaches rely heavily on serendipity and are hard to scale. [2/8]

Strategizing the search for bio-utility: A framework for evolution-integrated in silico bioprospecting To accurately and efficiently identify instances of useful biological variation, we must establish an evolution-integrated bioprospecting framework. This will enable us to better interpret biological ...

Really excited to share my first pub from my work at @arcadiascience.com - Strategizing the search for bio-utility: A framework for evolution-integrated in silico bioprospecting thestacks.org/publications... [1/8] 🧵

Interested in whether protein language models can learn about evolution and leverage this to predict protein structures? Check out the pub!

I'm very excited to share that today is my last day working at UC Berkeley before I start my new position at @arcadiascience.com next week! It has been a pleasure working as a postdoc in so many amazing labs along side amazing scientists, and I can't wait to start this new chapter!

I am recruiting PhD students to join my lab at MSU starting Fall 2026! Please spread the word and reach out if you are interested and/or want to learn more!

New Genome Assemblies for Poeciliidae: A Foundation for Adaptation Studies Abstract. Multiple lineages in the family Poeciliidae have independently adapted to hydrogen-sulfide-rich springs. The independent colonizations of such sp

Ryan, @rishidekayne.bsky.social et al. present six new chromosome-level genome assemblies for Poeciliidae, providing a foundation for studies on convergent evolution, repeat content, and demographic history.

🔗 academic.oup.com/gbe/article/17/6/evaf111/8169767

#genome #evolution

Top: Topology weightings across chr15 showing how the karamu haplotype is related to the klugii and orientis haplotypes. Upper panel shows three possible rooted genealogical topologies. Second panel shows weights for each topology along the chromosome, smoothed with a 20 kb span. Arrows above the plot indicate the locations of inversions. Third panel shows unsmoothed topology weightings across a 1.5 Mb region corresponding to Inversion 2. Bottom: Ancestry painting across a 100 kb region within Inversion 2, showing ancestry tracts for two homozygous karamu individuals compared to two representative individuals homozygous for the orientis and klugii haplotypes. Coding regions are indicated below the plot, with the candidate gene for background colouration yellow indicated. Green triangles represent the top 10 SNPs for background colour in our GWAS. There is evidence for recombination throughout the supergene region, and specifically in the vicinity of yellow, consistent with the hypothesis that orientis ancestry at this locus (i.e., the B allele) is associated with darker colouration in karamu individuals.

Dynamics of a supergene. A study of the BC supergene in wing color morphs of the African monarch #butterfly by @rishidekayne.bsky.social &co reveals dynamic evolution of #supergene haplotypes, fueled by incomplete recombination suppression 🧪 @plosbiology.org plos.io/3DiFhnL

Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces Snow leopards, Panthera uncia , are under threat from numerous pressures and are the focus of a great deal of conservation efforts. However, their elusive nature makes it difficult to estimate populat...

Happy that this paper - www.biorxiv.org/content/10.1... - was accepted at Mol Ecol Res and excited about the promise of this technology to measure pop sizes for such elusive species as snow leopards + learn about at least 1st-degree relationships + beyond? Congrats to Katie Solari and other authors!

Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes Abstract. Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve thes

Very excited to share our latest paper "Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes" 🐟 academic.oup.com/gbe/article/...

Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Thrilled to share a new lab pre-print from graduate student Tris Dodge! Tris & co elegantly uncover the genetic underpinnings and fitness consequences of a sexual mimicry polymorphism in Xiphophorus birchmanni: www.biorxiv.org/content/10.1...

Excited to share our review paper "Why Do Some Lineages Radiate While Others Do Not? Perspectives for Future Research on Adaptive Radiations" which is now online here: cshperspectives.cshlp.org/content/earl... Check it out for all things adaptive radiation! 🐟🦎🌿🦋

Hi everyone! It's about time I introduced myself - I'm Rishi and I'm doing a Postdoc at UC Santa Cruz working on adaptation genomics in Poeciliid fishes and Danaus butterflies. I'm particularly the role(s) of structural variation in evolution! 🧬 🧪